Construct surface model from atomic force microscope data
Probably long time since this is done but here goes:
open your AFM data with Gwyddion.net, export as ascii txt file, use open SCAD to plot the data and export as STL file. Import STL file into blender or your 3D printer slicer (to get the gcode for example). 

Gwyddion and openSCAD are python scryptable as far as I remember. Will work better on *ix systems than windows.